Interaction between sugarcane and Colletotrichum falcatum causing red rot: Understanding disease resistance at transcription level

Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot

Introduction

Sugarcane is one of the most important sugar crops worldwide, however, sugarcane production is seriously limited by sugarcane red rot, a soil-borne disease caused by Colletotrichum falcatum. Bacillus velezensis YC89 was isolated from sugarcane leaves and can significantly inhibited red rot disease caused by C. falcatum.

Methods

In this study, the genome of YC89 strain was sequenced, its genome structure and function were analyzed using various bioinformatics software, and its genome was compared with those of other homologous strains. In addition, the effectiveness of YC89 against sugarcane red rot and the evaluation of sugarcane plant growth promotion were also investigated by pot experiments.

Results

Here, we present the complete genome sequence of YC89, which consists of a 3.95 Mb circular chromosome with an average GC content of 46.62%. The phylogenetic tree indicated that YC89 is closely related to B. velezensis GS-1. Comparative genome analysis of YC89 with other published strains (B. velezensis FZB42, B. velezensis CC09, B. velezensis SQR9, B. velezensis GS-1, and B. amyloliquefaciens DSM7) revealed that the strains had a part common coding sequences (CDS) in whereas 42 coding were unique of strain YC89. Whole-genome sequencing revealed 547 carbohydrate-active enzymes and identified 12 gene clusters encoding secondary metabolites. Additionally, functional analysis of the genome revealed numerous gene/gene clusters involved in plant growth promotion, antibiotic resistance, and resistance inducer synthesis. In vitro pot tests indicated that YC89 strain controlled sugarcane red rot and promoted the growth of sugarcane plants. Additionally, it increased the activity of enzymes involved in plant defense, such as superoxide dismutase, peroxidase, polyphenol oxidase, chitinase, and β-1,3-glucanase.

Discussion

These findings will be helpful for further studies on the mechanisms of plant growth promotion and biocontrol by B. velezensis and provide an effective strategy for controlling red rot in sugarcane plants.

Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane

Red rot caused by the fungus Colletotrichum falcatum is the main disease limiting sugarcane productivity in several countries including the major producer India. The genetic basis for red rot resistance is unclear. We studied a panel of 305 sugarcane clones from the Australian breeding program for disease response phenotype and genotype using an Affymetrix® Axiom® array, to better understand the genetic basis of red rot resistance. SNP markers highly significantly associated with red rot response (≤ 10-8) were identified. Markers with largest effect were located in a single 14.6 Mb genomic region of sorghum (the closest diploid relative of sugarcane with a sequenced genome) suggesting the presence of a major-effect QTL. By genomic selection, the estimated selection accuracy was ~0.42 for red rot resistance. This was increased to ~0.5 with the addition of 29 highly significant SNPs as fixed effects. Analysis of genes nearby the markers linked to the QTL revealed many biotic stress responsive genes within this QTL, with the most significant SNP co-locating with a cluster of four chitinase A genes. The SNP markers identified here could be used to predict red rot resistance with high accuracy at any stage in the sugarcane breeding program.

Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum

The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.

Yield and technological quality of sugarcane cultivars under infestation of Diatraea saccharalis (Fabr., 1794)

ABSTRACT: The sugarcane borer, Diatraea saccharalis (Fabr., 1794) (Lepidoptera: Crambidae), is one of the main pests of sugarcane. This pest can reduce the quality and yield of the crop. Information on the quality and yield of cultivars in relation to the attack of sugarcane borer are necessary, since they guide the choice of the best materials for use in joint with other management tactics. Two field experiments were conducted in 2011 and 2012 to compare the quality and yield of 16 commercial sugarcane cultivars (IACSP93-3046, IACSP94-2094, IACSP94-2101, IAC91-1099, IACSP95-5000, IAC87-3396, RB92579, RB867515, RB966928, CTC2, CTC4, CTC9, CTC11, CTC15, CTC18 and SP86-0042) relative to the natural infestation of D. saccharalis. The experimental design was a randomized complete block with four replications. There was no difference between treatments for infestation index, with averages of 1.2 to 8.7% of bored internodes. Higher percentages of internodes with red rot were observed for CTC9, CTC2 and RB966928. The cultivars CTC4 and RB92579 infested with D. saccharalis resulted in lower technological quality, due the reduction in the contents of brix, apparent sucrose content (POL) and purity; and increase of the reducing sugars and, consequently, lower theoretically recoverable sugar (TRS). On the other hand, the lowest yields (t of cane ha-1) were observed for CTC18, IACSP94-2094, IACSP94-2101 and RB966928. Therefore, according to the hierarchical cluster analysis (UPGMA), the cultivars RB867515, CTC11, IAC91-1099, CTC15, SP86-0042, CTC2 and IACSP94-3046 were resistant to D. saccharalis.